Starting phenix.real_space_refine on Sat Jul 4 19:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zp9_14851/07_2026/7zp9_14851.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 Mg 8 5.21 5 S 140 5.16 5 C 14942 2.51 5 N 3628 2.21 5 O 4359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23097 Number of models: 1 Model: "" Number of chains: 34 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "I" Number of atoms: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 bond proxies already assigned to first conformer: 3407 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "M" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 bond proxies already assigned to first conformer: 3407 Chain: "G" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 316 Unusual residues: {' K': 1, 'LMT': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 6.04, per 1000 atoms: 0.26 Number of scatterers: 23097 At special positions: 0 Unit cell: (93.903, 115.509, 172.017, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 140 16.00 P 16 15.00 Mg 8 11.99 O 4359 8.00 N 3628 7.00 C 14942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 12 sheets defined 68.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 14 through 27 removed outlier: 3.520A pdb=" N SER H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 46 removed outlier: 3.713A pdb=" N GLY H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 80 through 94 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 122 through 137 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.762A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'E' and resid 14 through 28 Processing helix chain 'E' and resid 37 through 46 removed outlier: 4.232A pdb=" N GLY E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 14 through 28 Processing helix chain 'F' and resid 37 through 46 removed outlier: 4.024A pdb=" N GLY F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'F' and resid 67 through 70 Processing helix chain 'F' and resid 80 through 95 Processing helix chain 'F' and resid 105 through 116 Processing helix chain 'F' and resid 122 through 137 Processing helix chain 'I' and resid 23 through 44 removed outlier: 3.527A pdb=" N PHE I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) Proline residue: I 38 - end of helix removed outlier: 3.530A pdb=" N THR I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 67 Processing helix chain 'I' and resid 75 through 80 removed outlier: 3.612A pdb=" N PHE I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 122 Processing helix chain 'I' and resid 133 through 165 removed outlier: 3.711A pdb=" N ARG I 159 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 167 through 182 Processing helix chain 'I' and resid 199 through 214 Processing helix chain 'I' and resid 216 through 227 Processing helix chain 'I' and resid 230 through 234 Processing helix chain 'I' and resid 235 through 261 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 271 through 286 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 300 through 314 Processing helix chain 'I' and resid 325 through 341 Processing helix chain 'I' and resid 354 through 383 Processing helix chain 'I' and resid 386 through 399 Processing helix chain 'I' and resid 407 through 411 Processing helix chain 'I' and resid 412 through 439 Proline residue: I 430 - end of helix Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.841A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'B' and resid 14 through 27 Processing helix chain 'B' and resid 37 through 46 removed outlier: 3.684A pdb=" N GLY B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'J' and resid 14 through 27 removed outlier: 3.535A pdb=" N SER J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 46 removed outlier: 4.242A pdb=" N GLY J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 65 Processing helix chain 'J' and resid 80 through 94 Processing helix chain 'J' and resid 105 through 116 Processing helix chain 'J' and resid 122 through 137 Processing helix chain 'L' and resid 14 through 28 removed outlier: 3.619A pdb=" N SER L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 46 removed outlier: 4.247A pdb=" N GLY L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 66 Processing helix chain 'L' and resid 67 through 70 Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.549A pdb=" N SER L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 116 Processing helix chain 'L' and resid 122 through 137 Processing helix chain 'M' and resid 23 through 45 Proline residue: M 38 - end of helix removed outlier: 3.771A pdb=" N THR M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 45 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 67 Processing helix chain 'M' and resid 75 through 80 removed outlier: 3.686A pdb=" N PHE M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 122 removed outlier: 3.582A pdb=" N GLN M 99 " --> pdb=" O GLY M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 165 removed outlier: 3.845A pdb=" N ARG M 159 " --> pdb=" O PHE M 155 " (cutoff:3.500A) Proline residue: M 162 - end of helix Processing helix chain 'M' and resid 165 through 182 removed outlier: 3.593A pdb=" N PHE M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 214 Processing helix chain 'M' and resid 216 through 227 Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 235 through 261 Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 286 Processing helix chain 'M' and resid 295 through 299 Processing helix chain 'M' and resid 300 through 314 Processing helix chain 'M' and resid 325 through 342 Processing helix chain 'M' and resid 354 through 383 Processing helix chain 'M' and resid 386 through 399 Processing helix chain 'M' and resid 412 through 439 removed outlier: 3.537A pdb=" N TYR M 417 " --> pdb=" O GLU M 413 " (cutoff:3.500A) Proline residue: M 430 - end of helix Processing helix chain 'C' and resid 23 through 44 removed outlier: 3.527A pdb=" N PHE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Proline residue: C 38 - end of helix removed outlier: 3.530A pdb=" N THR C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.612A pdb=" N PHE C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 122 Processing helix chain 'C' and resid 133 through 165 removed outlier: 3.711A pdb=" N ARG C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 235 through 261 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 354 through 383 Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 439 Proline residue: C 430 - end of helix Processing helix chain 'G' and resid 23 through 45 Proline residue: G 38 - end of helix removed outlier: 3.771A pdb=" N THR G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 67 Processing helix chain 'G' and resid 75 through 80 removed outlier: 3.686A pdb=" N PHE G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 122 removed outlier: 3.581A pdb=" N GLN G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 165 removed outlier: 3.845A pdb=" N ARG G 159 " --> pdb=" O PHE G 155 " (cutoff:3.500A) Proline residue: G 162 - end of helix Processing helix chain 'G' and resid 165 through 182 removed outlier: 3.593A pdb=" N PHE G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 214 Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 235 through 261 Proline residue: G 246 - end of helix Processing helix chain 'G' and resid 271 through 286 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 300 through 314 Processing helix chain 'G' and resid 325 through 342 Processing helix chain 'G' and resid 354 through 383 Processing helix chain 'G' and resid 386 through 399 Processing helix chain 'G' and resid 412 through 439 removed outlier: 3.537A pdb=" N TYR G 417 " --> pdb=" O GLU G 413 " (cutoff:3.500A) Proline residue: G 430 - end of helix Processing sheet with id=AA1, first strand: chain 'H' and resid 50 through 53 removed outlier: 6.167A pdb=" N VAL H 31 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE H 52 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA H 33 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET H 72 " --> pdb=" O GLN H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 50 through 53 removed outlier: 6.171A pdb=" N VAL D 31 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE D 52 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA D 33 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 8 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL D 34 " --> pdb=" O PHE D 8 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL D 10 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN D 7 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N MET D 74 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA D 9 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 99 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 121 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 101 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 119 through 121 removed outlier: 3.829A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL E 31 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE E 52 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA E 33 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA E 54 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP E 35 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 119 through 121 removed outlier: 3.771A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL F 31 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE F 52 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 33 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA F 54 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP F 35 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 346 through 347 removed outlier: 4.464A pdb=" N VAL I 346 " --> pdb=" O VAL I 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR I 352 " --> pdb=" O ASP M 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.257A pdb=" N VAL A 31 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 52 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA A 33 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN A 7 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N MET A 74 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 9 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 99 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 121 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 101 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.120A pdb=" N VAL B 31 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE B 52 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 33 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE B 8 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 34 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 10 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN B 7 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N MET B 74 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA B 9 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 99 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 121 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 101 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 119 through 121 removed outlier: 6.183A pdb=" N VAL J 73 " --> pdb=" O TRP J 100 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS J 102 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL J 31 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE J 52 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA J 33 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 54 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP J 35 " --> pdb=" O ALA J 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 119 through 121 removed outlier: 6.577A pdb=" N VAL L 99 " --> pdb=" O HIS L 119 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE L 121 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL L 101 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 73 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET L 72 " --> pdb=" O GLN L 7 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL L 31 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE L 52 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA L 33 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA L 54 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP L 35 " --> pdb=" O ALA L 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 346 through 347 removed outlier: 4.421A pdb=" N VAL M 346 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 347 removed outlier: 4.464A pdb=" N VAL C 346 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR C 352 " --> pdb=" O ASP G 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 346 through 347 removed outlier: 4.421A pdb=" N VAL G 346 " --> pdb=" O VAL G 353 " (cutoff:3.500A) 1451 hydrogen bonds defined for protein. 4266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4052 1.33 - 1.45: 5708 1.45 - 1.57: 13429 1.57 - 1.69: 28 1.69 - 1.81: 261 Bond restraints: 23478 Sorted by residual: bond pdb=" N PRO H 123 " pdb=" CD PRO H 123 " ideal model delta sigma weight residual 1.473 1.729 -0.256 1.40e-02 5.10e+03 3.34e+02 bond pdb=" C4 ADP J 301 " pdb=" C5 ADP J 301 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" N PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C5 ADP A1002 " pdb=" C6 ADP A1002 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 23473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 29897 2.16 - 4.32: 1407 4.32 - 6.48: 304 6.48 - 8.63: 61 8.63 - 10.79: 83 Bond angle restraints: 31752 Sorted by residual: angle pdb=" N GLU F 93 " pdb=" CA GLU F 93 " pdb=" C GLU F 93 " ideal model delta sigma weight residual 111.69 105.83 5.86 1.23e+00 6.61e-01 2.27e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.37 -8.95 1.99e+00 2.53e-01 2.02e+01 angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.33 -8.91 1.99e+00 2.53e-01 2.01e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.54 5.35 1.24e+00 6.50e-01 1.86e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.54 5.35 1.24e+00 6.50e-01 1.86e+01 ... (remaining 31747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 13033 33.64 - 67.27: 372 67.27 - 100.91: 16 100.91 - 134.54: 5 134.54 - 168.18: 6 Dihedral angle restraints: 13432 sinusoidal: 5468 harmonic: 7964 Sorted by residual: dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual 300.00 131.82 168.18 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP A1002 " pdb=" O5' ADP A1002 " pdb=" PA ADP A1002 " pdb=" O2A ADP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 100.86 -160.86 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP L 301 " pdb=" O5' ADP L 301 " pdb=" PA ADP L 301 " pdb=" O2A ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 100.11 -160.11 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 13429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3651 0.107 - 0.213: 285 0.213 - 0.320: 42 0.320 - 0.426: 0 0.426 - 0.533: 8 Chirality restraints: 3986 Sorted by residual: chirality pdb=" CA THR M 288 " pdb=" N THR M 288 " pdb=" C THR M 288 " pdb=" CB THR M 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" CA THR G 288 " pdb=" N THR G 288 " pdb=" C THR G 288 " pdb=" CB THR G 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA THR I 288 " pdb=" N THR I 288 " pdb=" C THR I 288 " pdb=" CB THR I 288 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 7.00e+00 ... (remaining 3983 not shown) Planarity restraints: 3662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C MET M 92 " 0.040 2.00e-02 2.50e+03 pdb=" O MET M 92 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN M 93 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 92 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C MET G 92 " -0.040 2.00e-02 2.50e+03 pdb=" O MET G 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN G 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 86 " -0.010 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C LEU F 86 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU F 86 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA F 87 " -0.013 2.00e-02 2.50e+03 ... (remaining 3659 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.04: 20 2.04 - 2.82: 6254 2.82 - 3.59: 38649 3.59 - 4.37: 70897 4.37 - 5.14: 123080 Nonbonded interactions: 238900 Sorted by model distance: nonbonded pdb=" OE1 GLU F 64 " pdb=" CA GLY C 8 " model vdw 1.266 3.440 nonbonded pdb=" OE1 GLU L 64 " pdb=" CA GLY G 8 " model vdw 1.404 3.440 nonbonded pdb=" OE2 GLU L 64 " pdb=" N GLY G 8 " model vdw 1.471 3.120 nonbonded pdb=" OE2 GLU F 64 " pdb=" N GLY C 8 " model vdw 1.577 3.120 nonbonded pdb=" OE1 GLU L 38 " pdb=" OH TYR G 11 " model vdw 1.778 3.040 ... (remaining 238895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 137) selection = (chain 'B' and resid 6 through 137) selection = (chain 'D' and resid 6 through 137) selection = (chain 'E' and resid 6 through 137) selection = (chain 'F' and resid 6 through 137) selection = (chain 'H' and resid 6 through 137) selection = (chain 'J' and resid 6 through 137) selection = (chain 'L' and resid 6 through 137) } ncs_group { reference = (chain 'C' and (resid 7 through 15 or resid 21 through 350 or resid 352 through \ 455 or resid 503 through 510)) selection = (chain 'G' and (resid 7 through 15 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503 through 510)) selection = (chain 'I' and (resid 7 through 15 or resid 21 through 350 or resid 352 through \ 455 or resid 503 through 510)) selection = (chain 'M' and (resid 7 through 15 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503 through 510)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.640 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.256 23478 Z= 0.466 Angle : 1.130 10.792 31752 Z= 0.557 Chirality : 0.065 0.533 3986 Planarity : 0.004 0.047 3662 Dihedral : 15.069 168.179 8292 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.21 % Favored : 97.58 % Rotamer: Outliers : 0.88 % Allowed : 1.14 % Favored : 97.98 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 2766 helix: 1.44 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.26 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 15 TYR 0.014 0.001 TYR F 70 PHE 0.026 0.001 PHE I 210 TRP 0.011 0.001 TRP G 337 HIS 0.005 0.001 HIS G 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.47 (23478) covalent geometry : angle 1.12970 / 0.56 (31752) hydrogen bonds : bond 0.18893 / 12.95 ( 1451) hydrogen bonds : angle 6.61529 / 4.68 ( 4266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 516 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: H 59 GLU cc_start: 0.8137 (pt0) cc_final: 0.7850 (pt0) REVERT: F 130 ARG cc_start: 0.6899 (ttt90) cc_final: 0.6655 (ttt90) REVERT: I 139 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7499 (tptp) REVERT: I 299 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: I 354 ASN cc_start: 0.8260 (p0) cc_final: 0.7879 (p0) REVERT: A 22 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7894 (tptp) REVERT: M 139 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7288 (tptp) REVERT: M 296 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8238 (mt) REVERT: M 299 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: C 139 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7493 (tptp) REVERT: C 299 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: C 354 ASN cc_start: 0.8247 (p0) cc_final: 0.7855 (p0) REVERT: G 139 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7284 (tptp) REVERT: G 296 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (mt) REVERT: G 299 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7995 (m-80) outliers start: 20 outliers final: 4 residues processed: 532 average time/residue: 0.6994 time to fit residues: 416.1643 Evaluate side-chains 434 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 424 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 GLN D 50 GLN D 113 GLN F 108 GLN I 119 GLN I 263 ASN A 113 GLN B 30 GLN B 37 ASN B 50 GLN B 113 GLN J 108 GLN M 263 ASN M 301 GLN M 342 GLN C 119 GLN C 263 ASN G 263 ASN G 301 GLN G 342 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103239 restraints weight = 33922.591| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.92 r_work: 0.3007 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23478 Z= 0.155 Angle : 0.683 7.945 31752 Z= 0.322 Chirality : 0.044 0.180 3986 Planarity : 0.004 0.038 3662 Dihedral : 13.072 174.234 3494 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.06 % Favored : 97.87 % Rotamer: Outliers : 1.89 % Allowed : 9.14 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.16), residues: 2766 helix: 2.23 (0.12), residues: 1780 sheet: 1.48 (0.27), residues: 286 loop : 0.11 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 130 TYR 0.016 0.001 TYR F 70 PHE 0.034 0.002 PHE C 210 TRP 0.013 0.001 TRP M 227 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (23478) covalent geometry : angle 0.68303 / 0.32 (31752) hydrogen bonds : bond 0.04842 / 3.29 ( 1451) hydrogen bonds : angle 4.55554 / 3.22 ( 4266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 438 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: H 60 GLU cc_start: 0.8062 (mp0) cc_final: 0.7835 (mp0) REVERT: E 38 GLU cc_start: 0.8042 (tt0) cc_final: 0.7763 (tt0) REVERT: I 26 ARG cc_start: 0.7770 (ttt90) cc_final: 0.7024 (ttt-90) REVERT: I 139 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7601 (tptp) REVERT: I 307 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8822 (tpp) REVERT: A 22 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8148 (tptp) REVERT: B 22 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8148 (tptp) REVERT: B 130 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7930 (mmm160) REVERT: J 30 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7843 (mm110) REVERT: L 66 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7575 (ttmm) REVERT: M 139 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7437 (tptt) REVERT: M 299 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: C 26 ARG cc_start: 0.7779 (ttt90) cc_final: 0.7033 (ttt-90) REVERT: C 139 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7601 (tptp) REVERT: G 139 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7402 (tptt) REVERT: G 299 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8234 (m-80) outliers start: 43 outliers final: 12 residues processed: 464 average time/residue: 0.6608 time to fit residues: 344.2247 Evaluate side-chains 434 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 417 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 239 optimal weight: 0.1980 chunk 224 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 113 GLN E 82 ASN F 108 GLN I 263 ASN A 113 GLN B 37 ASN B 113 GLN L 108 GLN M 198 ASN M 263 ASN G 198 ASN G 263 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100867 restraints weight = 38809.743| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.05 r_work: 0.2964 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23478 Z= 0.181 Angle : 0.680 7.889 31752 Z= 0.318 Chirality : 0.044 0.187 3986 Planarity : 0.004 0.038 3662 Dihedral : 12.525 176.547 3484 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Rotamer: Outliers : 2.77 % Allowed : 11.20 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.16), residues: 2766 helix: 2.35 (0.12), residues: 1774 sheet: 1.18 (0.27), residues: 274 loop : 0.13 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 106 TYR 0.016 0.002 TYR F 70 PHE 0.035 0.002 PHE I 210 TRP 0.009 0.001 TRP C 337 HIS 0.004 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (23478) covalent geometry : angle 0.68037 / 0.32 (31752) hydrogen bonds : bond 0.04567 / 3.10 ( 1451) hydrogen bonds : angle 4.36177 / 3.08 ( 4266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 429 time to evaluate : 0.772 Fit side-chains REVERT: H 60 GLU cc_start: 0.8124 (mp0) cc_final: 0.7916 (mp0) REVERT: E 38 GLU cc_start: 0.8175 (tt0) cc_final: 0.7962 (tt0) REVERT: F 30 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7890 (mm110) REVERT: F 38 GLU cc_start: 0.8029 (tt0) cc_final: 0.7809 (tt0) REVERT: I 26 ARG cc_start: 0.7879 (ttt90) cc_final: 0.7039 (ttt-90) REVERT: I 139 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7592 (tptp) REVERT: I 228 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7752 (ttm110) REVERT: I 299 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (m-10) REVERT: A 22 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8339 (tptp) REVERT: B 130 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7983 (mmm160) REVERT: J 30 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7819 (mm110) REVERT: M 139 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7383 (tptp) REVERT: M 170 MET cc_start: 0.8436 (mmm) cc_final: 0.8199 (mmp) REVERT: M 296 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7936 (mt) REVERT: M 299 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: C 26 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7062 (ttt-90) REVERT: C 139 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7593 (tptp) REVERT: C 228 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7765 (ttm110) REVERT: C 299 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8316 (m-10) REVERT: G 139 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7347 (tptp) REVERT: G 170 MET cc_start: 0.8408 (mmm) cc_final: 0.8157 (mmp) REVERT: G 296 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7949 (mt) REVERT: G 299 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8190 (m-80) outliers start: 63 outliers final: 33 residues processed: 469 average time/residue: 0.6676 time to fit residues: 351.7949 Evaluate side-chains 457 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 416 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 194 MET Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 360 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 194 MET Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 360 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 243 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 GLN D 113 GLN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN B 37 ASN J 108 GLN L 108 GLN M 198 ASN M 263 ASN G 198 ASN G 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102479 restraints weight = 30730.580| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.72 r_work: 0.2977 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23478 Z= 0.132 Angle : 0.625 7.430 31752 Z= 0.291 Chirality : 0.042 0.174 3986 Planarity : 0.003 0.038 3662 Dihedral : 11.926 176.612 3480 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.68 % Rotamer: Outliers : 2.02 % Allowed : 12.74 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.16), residues: 2766 helix: 2.47 (0.12), residues: 1774 sheet: 1.13 (0.27), residues: 274 loop : 0.12 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 106 TYR 0.012 0.001 TYR F 70 PHE 0.033 0.001 PHE C 210 TRP 0.010 0.001 TRP I 337 HIS 0.005 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (23478) covalent geometry : angle 0.62500 / 0.29 (31752) hydrogen bonds : bond 0.04029 / 2.73 ( 1451) hydrogen bonds : angle 4.21769 / 2.97 ( 4266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 426 time to evaluate : 0.858 Fit side-chains REVERT: H 60 GLU cc_start: 0.8039 (mp0) cc_final: 0.7836 (mp0) REVERT: E 38 GLU cc_start: 0.8106 (tt0) cc_final: 0.7870 (tt0) REVERT: F 38 GLU cc_start: 0.7932 (tt0) cc_final: 0.7698 (tt0) REVERT: F 68 ASP cc_start: 0.7992 (p0) cc_final: 0.7571 (p0) REVERT: I 26 ARG cc_start: 0.7828 (ttt90) cc_final: 0.7000 (ttt-90) REVERT: I 139 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7542 (tptp) REVERT: A 22 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8167 (tptp) REVERT: B 22 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8133 (tptp) REVERT: J 30 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7771 (mm110) REVERT: J 68 ASP cc_start: 0.8040 (p0) cc_final: 0.7602 (p0) REVERT: M 139 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7310 (tptp) REVERT: M 170 MET cc_start: 0.8288 (mmm) cc_final: 0.8023 (mmp) REVERT: M 296 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7986 (mt) REVERT: M 299 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: C 26 ARG cc_start: 0.7840 (ttt90) cc_final: 0.7014 (ttt-90) REVERT: C 139 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7559 (tptp) REVERT: G 139 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7291 (tptp) REVERT: G 170 MET cc_start: 0.8266 (mmm) cc_final: 0.7991 (mmp) REVERT: G 296 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8009 (mt) REVERT: G 299 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8155 (m-80) outliers start: 46 outliers final: 22 residues processed: 452 average time/residue: 0.6450 time to fit residues: 327.7375 Evaluate side-chains 435 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 407 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 260 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 271 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN I 263 ASN A 37 ASN A 50 GLN A 113 GLN J 82 ASN J 108 GLN M 263 ASN G 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101725 restraints weight = 49181.792| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.27 r_work: 0.2940 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23478 Z= 0.114 Angle : 0.591 7.379 31752 Z= 0.275 Chirality : 0.041 0.169 3986 Planarity : 0.003 0.038 3662 Dihedral : 11.160 179.056 3480 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 2.24 % Allowed : 13.49 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.16), residues: 2766 helix: 2.64 (0.12), residues: 1774 sheet: 1.18 (0.27), residues: 270 loop : 0.05 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 106 TYR 0.012 0.001 TYR M 108 PHE 0.032 0.001 PHE I 210 TRP 0.013 0.001 TRP I 337 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23478) covalent geometry : angle 0.59130 / 0.27 (31752) hydrogen bonds : bond 0.03659 / 2.47 ( 1451) hydrogen bonds : angle 4.07282 / 2.87 ( 4266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 447 time to evaluate : 0.565 Fit side-chains REVERT: D 130 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7909 (mmm160) REVERT: E 38 GLU cc_start: 0.7968 (tt0) cc_final: 0.7727 (tt0) REVERT: E 122 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: F 38 GLU cc_start: 0.7721 (tt0) cc_final: 0.7464 (tt0) REVERT: F 68 ASP cc_start: 0.7941 (p0) cc_final: 0.7468 (p0) REVERT: I 26 ARG cc_start: 0.7682 (ttt90) cc_final: 0.6910 (ttt-90) REVERT: I 139 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7489 (tptp) REVERT: I 199 ASP cc_start: 0.7686 (t0) cc_final: 0.6959 (m-30) REVERT: I 228 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7630 (ttm110) REVERT: A 7 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8231 (mt0) REVERT: A 22 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8072 (tptp) REVERT: B 22 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8053 (tptp) REVERT: J 68 ASP cc_start: 0.7934 (p0) cc_final: 0.7473 (p0) REVERT: J 122 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8395 (mtm) REVERT: L 122 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: M 139 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7285 (tptp) REVERT: M 170 MET cc_start: 0.8132 (mmm) cc_final: 0.7878 (mmp) REVERT: M 296 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8068 (mm) REVERT: M 299 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: C 26 ARG cc_start: 0.7681 (ttt90) cc_final: 0.6913 (ttt-90) REVERT: C 139 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7509 (tptp) REVERT: C 199 ASP cc_start: 0.7650 (t0) cc_final: 0.6939 (m-30) REVERT: C 228 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7664 (ttm110) REVERT: G 139 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7259 (tptp) REVERT: G 170 MET cc_start: 0.8094 (mmm) cc_final: 0.7844 (mmp) REVERT: G 296 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8091 (mm) REVERT: G 299 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8043 (m-80) outliers start: 51 outliers final: 20 residues processed: 476 average time/residue: 0.6760 time to fit residues: 362.5989 Evaluate side-chains 444 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 416 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 360 LYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 360 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 129 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN A 37 ASN A 113 GLN J 82 ASN J 108 GLN L 104 ASN M 263 ASN M 282 GLN M 292 ASN G 263 ASN G 282 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097463 restraints weight = 41742.704| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.20 r_work: 0.2899 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23478 Z= 0.165 Angle : 0.649 7.342 31752 Z= 0.305 Chirality : 0.043 0.182 3986 Planarity : 0.003 0.038 3662 Dihedral : 11.230 176.621 3478 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % Rotamer: Outliers : 2.55 % Allowed : 14.10 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.16), residues: 2766 helix: 2.54 (0.12), residues: 1778 sheet: 0.95 (0.27), residues: 282 loop : 0.17 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 130 TYR 0.012 0.002 TYR M 108 PHE 0.030 0.002 PHE I 210 TRP 0.015 0.001 TRP C 337 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (23478) covalent geometry : angle 0.64882 / 0.30 (31752) hydrogen bonds : bond 0.04127 / 2.80 ( 1451) hydrogen bonds : angle 4.14050 / 2.93 ( 4266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 433 time to evaluate : 0.875 Fit side-chains REVERT: H 118 ASP cc_start: 0.8598 (m-30) cc_final: 0.8373 (m-30) REVERT: D 130 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7939 (mmm160) REVERT: E 38 GLU cc_start: 0.7980 (tt0) cc_final: 0.7721 (tt0) REVERT: F 30 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7781 (mm110) REVERT: F 38 GLU cc_start: 0.7840 (tt0) cc_final: 0.7631 (tt0) REVERT: F 68 ASP cc_start: 0.8026 (p0) cc_final: 0.7591 (p0) REVERT: I 26 ARG cc_start: 0.7710 (ttt90) cc_final: 0.6926 (ttt-90) REVERT: I 139 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7546 (tptp) REVERT: I 199 ASP cc_start: 0.7699 (t0) cc_final: 0.6890 (m-30) REVERT: A 7 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8297 (mt0) REVERT: A 22 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8147 (tptp) REVERT: J 82 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7766 (t0) REVERT: M 139 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7315 (tptp) REVERT: M 299 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: M 451 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8262 (p) REVERT: C 26 ARG cc_start: 0.7743 (ttt90) cc_final: 0.6951 (ttt-90) REVERT: C 139 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7538 (tptp) REVERT: C 199 ASP cc_start: 0.7668 (t0) cc_final: 0.6869 (m-30) REVERT: G 139 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7308 (tptp) REVERT: G 299 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: G 451 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8235 (p) outliers start: 58 outliers final: 34 residues processed: 470 average time/residue: 0.6720 time to fit residues: 356.2816 Evaluate side-chains 460 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 420 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 194 MET Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 360 LYS Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 194 MET Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 360 LYS Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 160 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 275 optimal weight: 0.0370 chunk 182 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN A 37 ASN A 113 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 GLN M 282 GLN G 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104862 restraints weight = 33960.067| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.89 r_work: 0.2982 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23478 Z= 0.115 Angle : 0.594 7.197 31752 Z= 0.278 Chirality : 0.041 0.169 3986 Planarity : 0.003 0.037 3662 Dihedral : 10.620 174.896 3478 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.80 % Allowed : 15.16 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.16), residues: 2766 helix: 2.68 (0.12), residues: 1766 sheet: 1.02 (0.28), residues: 270 loop : -0.00 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 106 TYR 0.010 0.001 TYR G 108 PHE 0.032 0.001 PHE I 210 TRP 0.015 0.001 TRP C 337 HIS 0.005 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (23478) covalent geometry : angle 0.59439 / 0.28 (31752) hydrogen bonds : bond 0.03613 / 2.45 ( 1451) hydrogen bonds : angle 4.04328 / 2.86 ( 4266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 439 time to evaluate : 0.755 Fit side-chains REVERT: E 30 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7647 (mp-120) REVERT: E 68 ASP cc_start: 0.8033 (p0) cc_final: 0.7558 (p0) REVERT: F 38 GLU cc_start: 0.7925 (tt0) cc_final: 0.7698 (tt0) REVERT: F 68 ASP cc_start: 0.8069 (p0) cc_final: 0.7568 (p0) REVERT: I 26 ARG cc_start: 0.7760 (ttt90) cc_final: 0.6928 (ttt-90) REVERT: I 139 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7506 (tptp) REVERT: I 199 ASP cc_start: 0.7799 (t0) cc_final: 0.6954 (m-30) REVERT: A 7 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8360 (mt0) REVERT: A 22 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8175 (tptp) REVERT: B 22 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8128 (tptp) REVERT: M 139 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7319 (tptp) REVERT: M 247 LEU cc_start: 0.8582 (tp) cc_final: 0.8348 (mp) REVERT: M 299 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: C 26 ARG cc_start: 0.7793 (ttt90) cc_final: 0.6966 (ttt-90) REVERT: C 139 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7531 (tptp) REVERT: C 199 ASP cc_start: 0.7785 (t0) cc_final: 0.6956 (m-30) REVERT: G 139 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7301 (tptp) REVERT: G 247 LEU cc_start: 0.8548 (tp) cc_final: 0.8323 (mp) REVERT: G 299 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8054 (m-80) outliers start: 41 outliers final: 25 residues processed: 462 average time/residue: 0.6864 time to fit residues: 356.8867 Evaluate side-chains 452 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 423 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 72 optimal weight: 0.4980 chunk 275 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 115 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 192 optimal weight: 0.4980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 108 GLN A 37 ASN A 113 GLN L 108 GLN M 282 GLN G 282 GLN G 292 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104221 restraints weight = 42578.017| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.16 r_work: 0.2966 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23478 Z= 0.108 Angle : 0.584 7.064 31752 Z= 0.274 Chirality : 0.040 0.166 3986 Planarity : 0.003 0.037 3662 Dihedral : 10.251 175.156 3478 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.58 % Allowed : 15.95 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.16), residues: 2766 helix: 2.74 (0.12), residues: 1768 sheet: 1.11 (0.28), residues: 270 loop : -0.01 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 106 TYR 0.009 0.001 TYR I 108 PHE 0.031 0.001 PHE I 210 TRP 0.018 0.001 TRP I 337 HIS 0.006 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (23478) covalent geometry : angle 0.58368 / 0.27 (31752) hydrogen bonds : bond 0.03470 / 2.34 ( 1451) hydrogen bonds : angle 3.98347 / 2.82 ( 4266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 451 time to evaluate : 0.716 Fit side-chains REVERT: E 30 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7518 (mp-120) REVERT: E 68 ASP cc_start: 0.7962 (p0) cc_final: 0.7495 (p0) REVERT: F 38 GLU cc_start: 0.7689 (tt0) cc_final: 0.7443 (tt0) REVERT: F 68 ASP cc_start: 0.7988 (p0) cc_final: 0.7499 (p0) REVERT: F 122 MET cc_start: 0.8801 (mtp) cc_final: 0.8519 (mmm) REVERT: I 26 ARG cc_start: 0.7619 (ttt90) cc_final: 0.6864 (ttt-90) REVERT: I 139 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7462 (tptp) REVERT: I 199 ASP cc_start: 0.7733 (t0) cc_final: 0.6920 (m-30) REVERT: A 7 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8286 (mt0) REVERT: A 22 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8073 (tptp) REVERT: B 22 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8032 (tptp) REVERT: J 30 GLN cc_start: 0.8102 (mp-120) cc_final: 0.7894 (mm110) REVERT: J 93 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: L 30 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7565 (mp-120) REVERT: M 139 LYS cc_start: 0.8019 (ttpt) cc_final: 0.7272 (tptp) REVERT: M 299 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: C 26 ARG cc_start: 0.7648 (ttt90) cc_final: 0.6878 (ttt-90) REVERT: C 135 ARG cc_start: 0.6996 (ttp80) cc_final: 0.6308 (mtt90) REVERT: C 139 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7448 (tptp) REVERT: C 199 ASP cc_start: 0.7703 (t0) cc_final: 0.6905 (m-30) REVERT: G 139 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7264 (tptp) REVERT: G 299 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: G 451 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8191 (p) outliers start: 36 outliers final: 16 residues processed: 471 average time/residue: 0.6701 time to fit residues: 356.1956 Evaluate side-chains 450 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 427 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 4 optimal weight: 0.3980 chunk 236 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 169 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 ASN F 108 GLN I 275 GLN A 37 ASN A 113 GLN L 104 ASN L 108 GLN M 282 GLN C 275 GLN G 282 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104637 restraints weight = 30350.296| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.72 r_work: 0.3016 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23478 Z= 0.119 Angle : 0.595 7.098 31752 Z= 0.280 Chirality : 0.041 0.169 3986 Planarity : 0.003 0.037 3662 Dihedral : 10.079 174.490 3478 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.71 % Allowed : 16.30 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.16), residues: 2766 helix: 2.74 (0.12), residues: 1768 sheet: 1.08 (0.28), residues: 270 loop : -0.01 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 106 TYR 0.011 0.001 TYR M 108 PHE 0.031 0.001 PHE I 210 TRP 0.021 0.001 TRP I 337 HIS 0.006 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (23478) covalent geometry : angle 0.59473 / 0.28 (31752) hydrogen bonds : bond 0.03557 / 2.41 ( 1451) hydrogen bonds : angle 3.98054 / 2.82 ( 4266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 430 time to evaluate : 0.688 Fit side-chains REVERT: E 68 ASP cc_start: 0.8024 (p0) cc_final: 0.7561 (p0) REVERT: E 122 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8440 (mtm) REVERT: F 38 GLU cc_start: 0.7885 (tt0) cc_final: 0.7663 (tt0) REVERT: F 68 ASP cc_start: 0.8048 (p0) cc_final: 0.7543 (p0) REVERT: F 122 MET cc_start: 0.8825 (mtp) cc_final: 0.8573 (mmm) REVERT: I 26 ARG cc_start: 0.7707 (ttt90) cc_final: 0.6637 (ttt90) REVERT: I 139 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7520 (tptp) REVERT: I 199 ASP cc_start: 0.7799 (t0) cc_final: 0.6952 (m-30) REVERT: I 295 ASP cc_start: 0.8251 (t0) cc_final: 0.8019 (t0) REVERT: A 7 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8378 (mt0) REVERT: A 22 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8178 (tptp) REVERT: B 22 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8134 (tptp) REVERT: J 66 LYS cc_start: 0.7758 (mppt) cc_final: 0.7368 (mmtm) REVERT: J 93 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: L 30 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7606 (mp-120) REVERT: M 139 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7353 (tptp) REVERT: M 299 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: M 451 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8239 (p) REVERT: C 26 ARG cc_start: 0.7739 (ttt90) cc_final: 0.6678 (ttt90) REVERT: C 139 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7516 (tptp) REVERT: C 199 ASP cc_start: 0.7796 (t0) cc_final: 0.6963 (m-30) REVERT: G 139 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7337 (tptp) REVERT: G 299 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: G 451 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8195 (p) outliers start: 39 outliers final: 22 residues processed: 452 average time/residue: 0.6567 time to fit residues: 333.8791 Evaluate side-chains 451 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 421 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 185 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 108 GLN A 113 GLN L 108 GLN G 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106006 restraints weight = 32163.045| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.75 r_work: 0.3002 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23478 Z= 0.121 Angle : 0.598 7.038 31752 Z= 0.282 Chirality : 0.041 0.170 3986 Planarity : 0.003 0.037 3662 Dihedral : 9.980 172.854 3478 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.58 % Allowed : 16.65 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.16), residues: 2766 helix: 2.72 (0.12), residues: 1774 sheet: 1.08 (0.28), residues: 270 loop : 0.03 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 106 TYR 0.009 0.001 TYR G 108 PHE 0.030 0.001 PHE I 210 TRP 0.021 0.001 TRP I 337 HIS 0.005 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (23478) covalent geometry : angle 0.59842 / 0.28 (31752) hydrogen bonds : bond 0.03586 / 2.44 ( 1451) hydrogen bonds : angle 3.98071 / 2.82 ( 4266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 423 time to evaluate : 0.854 Fit side-chains REVERT: H 59 GLU cc_start: 0.8235 (pt0) cc_final: 0.7921 (mt-10) REVERT: E 68 ASP cc_start: 0.8030 (p0) cc_final: 0.7569 (p0) REVERT: E 130 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7559 (mtm180) REVERT: F 38 GLU cc_start: 0.7903 (tt0) cc_final: 0.7684 (tt0) REVERT: F 68 ASP cc_start: 0.8069 (p0) cc_final: 0.7565 (p0) REVERT: F 122 MET cc_start: 0.8832 (mtp) cc_final: 0.8582 (mmm) REVERT: I 26 ARG cc_start: 0.7770 (ttt90) cc_final: 0.6635 (ttt90) REVERT: I 139 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7549 (tptp) REVERT: I 199 ASP cc_start: 0.7807 (t0) cc_final: 0.6963 (m-30) REVERT: I 295 ASP cc_start: 0.8268 (t0) cc_final: 0.8048 (t0) REVERT: A 7 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8354 (mt0) REVERT: A 22 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8176 (tptp) REVERT: B 22 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8154 (tptp) REVERT: J 93 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: L 30 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7641 (mp-120) REVERT: M 139 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7383 (tptp) REVERT: M 299 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: M 451 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8214 (p) REVERT: C 26 ARG cc_start: 0.7805 (ttt90) cc_final: 0.6684 (ttt90) REVERT: C 139 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7537 (tptp) REVERT: C 199 ASP cc_start: 0.7806 (t0) cc_final: 0.6962 (m-30) REVERT: G 139 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7371 (tptp) REVERT: G 299 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: G 451 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8141 (p) outliers start: 36 outliers final: 22 residues processed: 447 average time/residue: 0.6732 time to fit residues: 338.8232 Evaluate side-chains 450 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 421 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 108 GLN A 113 GLN L 108 GLN G 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099978 restraints weight = 37468.266| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.07 r_work: 0.2995 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23478 Z= 0.146 Angle : 0.628 7.338 31752 Z= 0.297 Chirality : 0.042 0.177 3986 Planarity : 0.003 0.037 3662 Dihedral : 10.164 169.993 3478 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.63 % Allowed : 16.87 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.16), residues: 2766 helix: 2.67 (0.12), residues: 1768 sheet: 0.96 (0.28), residues: 282 loop : 0.08 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 106 TYR 0.008 0.001 TYR M 11 PHE 0.030 0.002 PHE I 210 TRP 0.025 0.001 TRP I 337 HIS 0.005 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (23478) covalent geometry : angle 0.62761 / 0.30 (31752) hydrogen bonds : bond 0.03843 / 2.62 ( 1451) hydrogen bonds : angle 4.04557 / 2.86 ( 4266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8945.52 seconds wall clock time: 153 minutes 6.41 seconds (9186.41 seconds total)